Upon the death of Mary of Burgundy in 1482, her substantial possessions including the Burgundian Netherlands passed to her son, Philip the Handsome. Through his father Maximilian I, Holy Roman Emperor from 1493, Philip was a Habsburg scion, and so the period of the Habsburg Netherlands began. The period 1481–1492 saw the Flemish cities revolt and Utrecht embroiled in civil war, but by the turn of the century both areas had been pacified by the Habsburg rulers.

Philip's son Charles V, born in Ghent, succeeded his father in 1506, when he still was a six-year-old minor. His grandfather Emperor Maximilian I incorporated the Burgundian heritage into the Burgundian Circle, whereafter the territories in the far west of the Empire developed a certain grade of autonomy. Attaining full age in 1515, Charles went on to rule his Burgundian heritage as a native Netherlander. He acquired the lands of Overijssel and the Bishopric of Utrecht (see Guelderian Wars), purchased Friesland from Duke George of Saxony and regained Groningen and Gelderland. His Seventeen Provinces were re-organised in the 1548 Burgundian Treaty, whereby the Imperial estates represented in the Imperial Diet at Augsburg acknowledged a certain autonomy of the Netherlands. It was followed by a pragmatic sanction by the Emperor the next year, which established the Seventeen Provinces as an entity separate from the Empire and from France.